4.6.3 prep, upstream propegation

CMakeLists.txt

@@ -737,6 +737,8 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
 
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pset_libver_bounds "" HDF5_HAS_LIBVER_BOUNDS)
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5free_memory "" HDF5_HAS_H5FREE)
+  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5allocate_memory "" HDF5_HAS_ALLOCATE_MEMORY)
+  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5resize_memory "" HDF5_HAS_RESIZE_MEMORY)
 
   IF(HDF5_PARALLEL)
 	SET(HDF5_CC h5pcc)

RELEASE_NOTES.md

@@ -7,10 +7,11 @@ This file contains a high-level description of this package's evolution. Release
 
 ## 4.6.3 - TBD
 
-## 4.6.2.1 - February 15, 2019
-
 ### Maintenance Release
-
+* Now always write hidden coordinates attribute, which allows faster file opens when present. See [Github #1262](https://github.com/Unidata/netcdf-c/issues/1262) for more information.
+* Some fixes for rename, including fix for renumbering of varids after a rename (#1307), renaming var to dim without coordinate var. See [Github #1297](https://github.com/Unidata/netcdf-c/issues/1297).
+* Fix of NULL parameter causing segfaults in put_vars functions. See [Github #1265](https://github.com/Unidata/netcdf-c/issues/1265) for more information.
+* Fix of --enable-benchmark benchmark tests [Github #1211](https://github.com/Unidata/netcdf-c/issues/1211)
 * Update the license from the home-brewed NetCDF license to the standard 3-Clause BSD License.  This change does not result in any new restrictions; it is merely the adoption of a standard, well-known and well-understood license in place of the historic NetCDF license written at Unidata.  This is part of a broader push by Unidata to adopt modern, standardized licensing.  
 * [BugFix] Corrected DAP-releated issues on big-endian machines. See [Github #1321](https://github.com/Unidata/netcdf-c/issues/1321), [Github #1302](https://github.com/Unidata/netcdf-c/issues/1302) for more information.
 * [BugFix][Enhancement]  Various and sundry bugfixes and performance enhancements, thanks to @edhartnett, @gsjaardema, @t-b, @wkliao, and all of our other contributors.

config.h.cmake.in

@@ -367,6 +367,12 @@ are set when opening a binary file on Windows. */
    nc4file. */
 #cmakedefine HDF5_HAS_H5FREE 1
 
+/* if true, H5allocate_memory() will be used. */
+#cmakedefine HDF5_HAS_ALLOCATE_MEMORY 1
+
+/* if true, H5resize_memory() will be used. */
+#cmakedefine HDF5_HAS_RESIZE_MEMORY 1
+
 /* if true, hdf5 has parallelism enabled */
 #cmakedefine HDF5_PARALLEL 1
 

configure.ac

@@ -1028,7 +1028,7 @@ if test "x$enable_hdf5" = xyes; then
 
    # H5Pset_fapl_mpiposix and H5Pget_fapl_mpiposix have been removed since HDF5 1.8.12.
    # Use H5Pset_fapl_mpio and H5Pget_fapl_mpio, instead.
-   AC_CHECK_FUNCS([H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5free_memory H5Pset_libver_bounds H5Pset_all_coll_metadata_ops])
+   AC_CHECK_FUNCS([H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5free_memory H5resize_memory H5allocate_memory H5Pset_libver_bounds H5Pset_all_coll_metadata_ops])
 
    # Check to see if HDF5 library has collective metadata APIs, (HDF5 >= 1.10.0)
    if test "x$ac_cv_func_H5Pset_all_coll_metadata_ops" = xyes; then
@@ -1062,6 +1062,14 @@ if test "x$enable_hdf5" = xyes; then
       AC_DEFINE([HDF5_HAS_H5FREE], [1], [if true, H5free_memory() will be used to free hdf5-allocated memory in nc4file.])
    fi
 
+   if test "x$ac_cv_func_H5allocate_memory" = xyes; then
+      AC_DEFINE([HDF5_HAS_ALLOCATE_MEMORY], [1], [if true, H5allocate_memory() will be used.])
+   fi
+
+   if test "x$ac_cv_func_H5resize_memory" = xyes; then
+      AC_DEFINE([HDF5_HAS_resize_MEMORY], [1], [if true, H5resize_memory() will be used.])
+   fi
+
    if test "x$ac_cv_func_H5Pset_libver_bounds" = xyes; then
       AC_DEFINE([HDF5_HAS_LIBVER_BOUNDS], [1], [if true, netcdf4 file properties will be set using H5Pset_libver_bounds])
    fi

plugins/H5Zbzip2.c

@@ -7,6 +7,8 @@
 /* Older versions of the hdf library may define H5PL_type_t here */
 #include <H5PLextern.h>
 
+#include "config.h"
+
 #ifndef DLL_EXPORT
 #define DLL_EXPORT
 #endif
@@ -90,7 +92,11 @@ size_t H5Z_filter_bzip2(unsigned int flags, size_t cd_nelmts,
 
     /* Prepare the output buffer. */
     outbuflen = nbytes * 3 + 1;  /* average bzip2 compression ratio is 3:1 */
+#ifdef HDF5_HAS_ALLOCATE_MEMORY
     outbuf = H5allocate_memory(outbuflen,0);
+#else
+    outbuf = (char*)malloc(outbuflen * sizeof(char));
+#endif
     if (outbuf == NULL) {
       fprintf(stderr, "memory allocation failed for bzip2 decompression\n");
       goto cleanupAndFail;
@@ -123,7 +129,11 @@ size_t H5Z_filter_bzip2(unsigned int flags, size_t cd_nelmts,
       if (ret != BZ_STREAM_END && stream.avail_out == 0) {
         /* Grow the output buffer. */
         newbuflen = outbuflen * 2;
+#ifdef HDF5_HAS_RESIZE_MEMORY
         newbuf = H5resize_memory(outbuf, newbuflen);
+#else
+        newbuf = realloc(outbuf,newbuflen);
+#endif
         if (newbuf == NULL) {
           fprintf(stderr, "memory allocation failed for bzip2 decompression\n");
           goto cleanupAndFail;
@@ -167,7 +177,12 @@ size_t H5Z_filter_bzip2(unsigned int flags, size_t cd_nelmts,
 
     /* Prepare the output buffer. */
     outbuflen = nbytes + nbytes / 100 + 600;  /* worst case (bzip2 docs) */
+#ifdef HDF5_HAS_ALLOCATE_MEMORY
     outbuf = H5allocate_memory(outbuflen,0);
+#else
+    outbuf = (char*)malloc(outbuflen * sizeof(char));
+#endif
+
     if (outbuf == NULL) {
       fprintf(stderr, "memory allocation failed for bzip2 compression\n");
       goto cleanupAndFail;
@@ -185,13 +200,23 @@ size_t H5Z_filter_bzip2(unsigned int flags, size_t cd_nelmts,
   }
 
   /* Always replace the input buffer with the output buffer. */
+#ifdef HDF5_HAS_H5FREE
   H5free_memory(*buf);
+#else
+  free(*buf);
+#endif
+
   *buf = outbuf;
   *buf_size = outbuflen;
   return outdatalen;
 
  cleanupAndFail:
   if (outbuf)
+#ifdef HDF5_HAS_H5FREE
     H5free_memory(outbuf);
+#else
+  free(outbuf);
+#endif
+
   return 0;
 }

plugins/H5Zmisc.c

@@ -8,6 +8,8 @@
 #include <H5PLextern.h>
 #include "h5misc.h"
 
+#include "config.h"
+
 #ifndef DLL_EXPORT
 #define DLL_EXPORT
 #endif
@@ -109,21 +111,37 @@ H5Z_filter_test(unsigned int flags, size_t cd_nelmts,
     if (flags & H5Z_FLAG_REVERSE) {
 
         /* Replace buffer */
+#ifdef HDF5_HAS_ALLOCATE_MEMORY
         newbuf = H5allocate_memory(*buf_size,0);
+#else
+        newbuf = malloc(*buf_size * sizeof(void));
+#endif
         if(newbuf == NULL) abort();
         memcpy(newbuf,*buf,*buf_size);
-	/* reclaim old buffer */
-	H5free_memory(*buf);
+        /* reclaim old buffer */
+#ifdef HDF5_HAS_H5FREE
+        H5free_memory(*buf);
+#else
+        free(*buf);
+#endif
         *buf = newbuf;
 
     } else {
 
         /* Replace buffer */
-        newbuf = H5allocate_memory(*buf_size,0);
-        if(newbuf == NULL) abort();
+#ifdef HDF5_HAS_ALLOCATE_MEMORY
+      newbuf = H5allocate_memory(*buf_size,0);
+#else
+      newbuf = malloc(*buf_size * sizeof(void));
+#endif
+      if(newbuf == NULL) abort();
         memcpy(newbuf,*buf,*buf_size);
 	/* reclaim old buffer */
-	H5free_memory(*buf);
+#ifdef HDF5_HAS_H5FREE
+        H5free_memory(*buf);
+#else
+        free(*buf);
+#endif
         *buf = newbuf;
 
     }